Mandal, Amit Kumar, Bisht, Shveta, Bhat, Vijay S, Krishnaswamy, Patnam Rajagopalan, Balaram, Padmanabhan
The clinical analysis of hemoglobin by ion exchange chromatography can result in ambiguities in identification of the nature of the globin chain present in patient samples. LC/ESI-MS provides rapid...
Nucleation, Growth, and Form in Crystals of Peptide Helices (2008)
Vasudev, Prema G, Narayanaswamy, Shamala, Balaram, Padmanabhan
A model for the nucleation of crystallization in peptide helices is presented. The crystal structures of four polymorphic forms of a hydrophobic helical decapeptide...
Thakur, Suman S, Balaram, Padmanabhan
The fragmentation of positive and negative ions of peptide disulfides under mass spectrometric conditions yields distinctly different product ion distributions. A negative ion upon collision induced...
Gowd, Konkallu Hanumae, Dewan, Kalyan Kumar, Lengar, Prathima, Krishnan, Kozhalmannom S, Balaram, Padmanabhan
The peptide library present in the venom of the piscivorous marine snail Conus achatinus has been probed using a combination of mass spectrometry and cDNA sequencing methods. Matrix assisted laser...
Saha, Indranil, Chatterjee, Bhaswati, Shamala, Narayanaswamy, Balaram, Padmanabhan
Multiple conformational states in heterochiral diproline sequences have been characterized in the solid state by the determination of the crystal structures of seven tripeptides in enantiomeric and...
Vasudev, Prema G, Rai, Rajkishor, Shamala, Narayanaswamy, Balaram, Padmanabhan
The author has brought to our attention the following revision for Table II of the article listed above, published in Biopolymers 2008, 90(2):138–150. See the revised table shown on the following...
Vasudev, Prema G, Rai, Rajkishor, Shamala, Narayanaswamy, Balaram, Padmanabhan
The conformational preferences of the 3,3-disubstituted \beta-amino acid residue, 1-aminocyclohexaneacetic acid $(\beta^{3,3}Ac_6c)$ have been investigated by determining the crystal structures of...
Chatterjee, Bhaswati, Saha, Indranil, Raghothama, Srinivasarao, Aravinda, Subrayashastry, Rai, Rajkishor, Shamala, Narayanaswamy, ...
Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has...
Tryptophan Rich Peptides: Influence of Indole Rings on Backbone Conformation (2007)
Mahalakshmi, Radhakrishnan, Sengupta, Anindita, Raghothama, Srinivasarao, Shamala, Narayanaswamy, Balaram, Padmanabhan
Synthetic peptides with defined secondary structure scaffolds, namely hairpins and helices, containing tryptophan residues, have been investigated in this study to probe the influence of a large...
Gowd, Konkallu Hanumae, Krishnan, KS, Balaram, Padmanabhan
Protein disulfide isomerase (PDI) has been identified in a protein extract from the venom duct of the marine snail C. amadis. In-gel tryptic digestion of a thick protein band at approximately 55 kDa...
Rai, Rajkishor, Vasudev, Prema G, Ananda, Kuppanna, Raghothama, Srinivasarao, Shamala, Narayanaswamy, Karle, Isabella L, ...
The \beta turn segment in designed peptide hairpins has been expanded by the insertion of \beta-, \gamma- and \delta amino acids at the i+2 position. The model octapeptides...
Mandal, Amit Kumar, Balaram, Padmanabhan
The formation of a pyroglutamyl residue by enzymatic cyclization of an amino terminus glutamine residue is a common posttranslational modification [1–3]. Several biologically active peptides, most...
NMR Analysis of Aromatic Interactions in Designed Peptide \beta -Hairpins (2006)
Mahalakshmi, Radhakrishnan, Raghothama, Srinivasa Rao, Balaram, Padmanabhan
Designed octapeptide \beta -hairpins containing a central $ ^DPro-Gly$ segment have been used as a scaffold to place the aromatic residues Tyr and Trp at various positions on the antiparallel \beta...
Sabareesh, Varatharajan, Balaram, Padmanabhan
The fragmentations of $[M+H]^+$ and $[M+Na]^+$ adducts of neutral peptides with blocked N- and C-termini have been investigated using electrospray ion trap mass spectrometry. The N-termini of these...
Conformational and Sequence Signatures in $\beta$ Helix Proteins (2006)
Iengar, Prathima, Joshi, NV, Balaram, Padmanabhan
$\beta$ helix proteins are characterized by a repetitive fold, in which the repeating unit is a $\beta$-helical coil formed by three strand segments linked by three loop segments. Using a data set of...
Roy, Rituparna S, Gopi, Hosahudya N, Raghothama, Srinivasa Rao, Karle, Isabella L, Balaram, Padmanabhan
The effects of inserting unsubstituted -amino acids into the strand segments of model -hairpin peptides was investigated by using four synthetic decapeptides,...
Design of a Peptide Hairpin Containing a Central Three-Residue Loop (2006)
Rai, Rajkishor, Raghothama, Srinivasarao, Balaram, Padmanabhan
The construction of a designed $\beta$-hairpin structure, containing a central three-residue loop has been successfully achieved in the synthetic nonapeptide...
Naval Research Reviews, Volume 46, February 1994 (2006)
Lugoski-Karle, Isabella, Karle, Jerome, Karle, I. L., Hauptman, H., Wing, A. B., Flippen-Anderson, Judith L., ...
Particle contents: Crystal and Molecular Structure of P,P'- Dimethoxybenzophenone by the Direct Probability Method; Crystal Structure of (Leu1) zervamicin, a membrane ion-channel peptide:...
Nair, Sudarslal Sadasivan, Nilsson, Carol L, Emmett, Mark R, Schaub, Tanner M, Gowd, Konkallu Hanumae, Thakur, Suman S, ...
T-1-family conotoxins belong to the T-superfamily and are composed of 10-17 amino acids. They share a common cysteine framework and disulfide connectivity and exhibit unusual posttranslational...
Rai, Rajkishor, Raghothama, Srinivasarao, Sridharan, Rajagopalan, Balaram, Padmanabhan
Designed octapeptides Boc-Leu-Val-Val-Aib-$^DXxx$-Leu-Val-Val-OMe $(^DXxx=^DAla, 3a; ^DVal, 3c$ and $^DPro, 5a)$ and Boc-Leu-Phe-Val-Aib-$^DAla$-Leu-Phe-Val-OMe (3b) have been investigated to...
Structural studies of model peptides \beta-, \gamma- containing and \delta- amino acids (2006)
Sengupta, Anindita, Aravinda, Subrayashastry, Shamala, Narayanaswamy, Raja, Muruga Poopathi K, Balaram, Padmanabhan
The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-\beta Gly-NHMe (2), Piv-Pro- \beta Gly-OMe (3), Piv-Pro- \delta Ava-OMe (4) and Boc-Pro- \gamma Abu-OH (5) are described...
A novel conotoxin modulating sodium channels (2005)
Balaram, Padmanabhan, Krishnan, Kozhalmannom Subramaniasastry
A 26 residue peptide (Am2766) with the sequence CKQAGESCDIFSQNCCVGTCAFICE-NH2 has been isolated and purified from the venom of the molluscivorous snail, Conus amadis, collected of the southeastern...
Plasmodium Falciparum Triosephosphate Isomerase: New Insights Into an Old Enzyme (2005)
Ravindra, Gudihal, Balaram, Padmanabhan
Triosephosphate isomerase (TIM), a central enzyme in the glycolytic pathway, has been the subject of extensive structural and mechanistic investigations over the past 30 years. The TIM barrel is the...
Ranjini, Arumugam Sri, Das, Puspendu K, Balaram, Padmanabhan
In this paper, a new application of the hyper-Rayleigh scattering technique in determining multiple binding constants of a small molecule like bilirubin to a macromolecule like the protein human...
Sampathkumar, Rangasamy, Balasubramanyam, Muthuswamy, Sudarslal, Sadasivannair, Rema, Mohan, Mohan, Viswanthan, Balaram, Padmanabhan
Objective: Protein glutathionylation is considered an important post-translational modification in the pathogenesis of complex diseases. The aim of this study was to examine whether hemoglobin (Hb)is...
Mahalakshmi, Radhakrishnan, Shanmugam, Ganesh, Polavarapu, Prasad L, Balaram, Padmanabhan
Carefullychosen peptide systems can provide valuable insights into the details of protein folding. Construction of the secondarystructures most commonlyobserved in proteins, namely a-helices and...
Roy, Rituparna S, Gopi, Hosahudya N, Raghothama, S, Gilardi, Richard D, Karle, Isabella L, Balaram, Padmanabhan
The incporation of \beta -amino acid residues into the strand segments of designed \beta -hairpin leads to the formation of polar sheets, since in the case of \beta -peptide strands, all adjacent...
Vasudev, Prema G, Shamala, Narayanaswamy, Ananda, Kuppanna, Balaram, Padmanabhan
The insertion of additional atoms into \alpha -polypeptide backbones by the introduction of \beta, \gamma, and higher \omega amino acid residues expands the range of polypeptide secondary...
Harini, Veldore Vidya, Aravinda, Subrayashastry, Rai, Rajkishor, Shamala, Narayanaswamy, Balaram, Padmanabhan
Peptide $\beta$-hairpin formation is facilitated by centrally positioned D-Pro-Xxx segments. The synthetic peptides Boc-Leu-Phe-Val-D-Pro-$Ac_6c$-Leu-Phe-Val-OMe (1) and...
Gudihal, Ravindra, Rappal, Ranganayaki S, Raghothama, Srinivasa, Mandayam, Srinivasan C, Gilardi, Richard D, Karle, Isabella L, ...
Two new cyclohexadepsipeptides have been isolated from the fungus Isaria. Fungal growth in solid media yielded hyphal strands from which peptide fractions were readily isolable by organic-solvent...
Sudarslal, Sadasivannair, Singaravadivelan, Govindaswamy, Ramasamy, Palanisamy, Ananda, Kuppanna, Sarma, Siddhartha P, Sikdar, Sujit K, ...
A novel 13-residue peptide Mo1659 has been isolated from the venom of a vermivorous cone snail, Conus monile. HPLC fractions of the venom extract yielded an intense UV absorbing fraction with a mass...
Aravinda, Subrayashastry, Harini, Veldore Vidya, Shamala, Narayanaswamy, Das, Chittaranjan, Balaram, Padmanabhan
De noVo designed ‚b-hairpin peptides have generally been recalcitrant to crystallization. The crystal structures of four synthetic peptide ‚b-hairpins, Boc-Leu-Val-Val-DPro-Gly-Leu-Phe-Val-OMe...
Hydrogen-Bond Lengths in Polypeptide Helices: No Evidence for Short Hydrogen Bonds (2004)
Aravinda, Subrayashastry, Datta, Saumen, Shamala, Narayanaswamy, Balaram, Padmanabhan
The $3_1_0$ helix and \alpha helix are closely related secondary structures observed in polypeptides. The $3_1_0$ helix is characterized by successive $4\rightarrow1$ $(C_1_0)$ hydrogen bonds...
Aravinda, Subrayashastry, Shamala, Narayanaswamy, Bandyopadhyay, Abhishek, Balaram, Padmanabhan
The structural characterization in crystals of three designed decapeptides containing a double D-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-...
Karle, Isabella L, Gopi, Hosahudya N, Balaram, Padmanabhan
The design of the synthetic 19-residue peptide Boc-Leu-Aib-Val-Ala-Leu5-Aib-Val-D-Ala-D-Leu-Leu10-Val-Phe-Val-Aib-D-Val15-Leu-Phe-Val-Val-OMe (Aib, alpha-aminoisobutyric acid; OMe, methyl ester) was...
Parthasarathy, Sampathkumar, Eaazhisai, Kandiah, Balaram, Hemalatha, Balaram, Padmanabhan, Murthy, Mathur RN
Triose-phosphate isomerase, a key enzyme of the glycolytic pathway, catalyzes the isomerization of dihydroxy acetone phosphate and glyceraldehyde 3-phosphate. In this communication we report the...
Pattanaik, Priyaranjan, Jain, Bimba, Ravindra, Gudihal, Gopi, Hosahudya N, Pal, Prajna P, Balaram, Hemalatha, ...
Novel internally quenched fluorescence peptide substrates containing sequence specific sites for cleavage by multiple proteases were designed and synthesized. The 28 and 29 residue peptides contain...
Aravinda, Subrayashastry, Ananda, Kuppanna, Shamala, Narayanaswamy, Balaram, Padmanabhan
The crystal structures of four dipeptides that contain the stereochemically constrained gamma-amino acid residue gabapentin (1-(aminomethyl) cyclohexaneacetic acid Gpn) are described. The molecular...
Aravinda, Subrayashastry, Shamala, Narayanaswamy, Das, Chittaranjan, Sriranjini, Arumugam, Karle, Isabella L, Balaram, Padmanabhan
Aromatic-aromatic interactions between phenylalanine side chains in peptides have been probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, I;...
Pattanaik, Priyaranjan, Ravindra, Gudihal, Sengupta, Chandana, Maithal, Kapil, Balaram, Padmanabhan, Balaram, Hemalatha
Plasmodium falciparum triosephosphate isomerase (PfTIM) contains two tryptophan residues, W11 and W168. One is positioned in the interior of the protein, and the other is located on the active-site...
Gopi, Hosahudya N, Ravindra, Gudihal, Pal, Prajna P, Pattanaik, Priyaranjan, Balaram, Hemalatha, Balaram, Padmanabhan
A set of designed internally quenched fluorescence peptide substrates has been used to probe the e¡ects of insertion of beta-peptide bonds into peptide sequences. The test sequence chosen...
Aravinda, Subrayashastry, Shamala, Narayanaswamy, Bandyopadhyay, Abhishek, Balaram, Padmanabhan
The structural characterization in crystals of three designed decapeptides containing a double D-segment at the C-terminus is described. The crystal structures of the peptides...
A right handed peptide helix containing a central double D-amino acid segment (2002)
Aravinda, Subrayashastry, Shamala, Narayanaswamy, Desiraju, Shrilakshmi, Balaram, Padmanabhan
The crystal structure of the 13 residue peptide Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-DAla-DLeu-Aib-Leu-Aib-Val-OMe reveals a continuous helical conformation providing an unambiguous characterization of...
Aravinda, Subrayashastry, Shamala, Narayanaswamy, Rajkishore, Rai, Gopi, Hosahudya N, Balaram, Padmanabhan
Recent progress in the design of beta-hairpin peptides[1] and beta-sheet models has been based on the ability to nucleate reverse turns of the appropriate stereochemistry. D-Pro-Gly[2] and to a...
Maithal, Kapil, Ravindra, Gudihal, Balaram, Hemalatha, Balaram, Padmanabhan
Plasmodium falciparum triose-phosphate isomerase, a homodimeric enzyme, contains four cysteine residues at positions 13, 126, 196, and 217 per subunit. Among these, Cys-13 is present at the dimer...
Cheung, Eugene Y, McCabe, Emma E, Harris, Kenneth DM, Johnston, Roy L, Tedesco, Emilio, Raja, Muruga Poopathi K, ...
The finding that peptides containing beta-amino acid residues give rise to folding patterns hitherto unobserved in alpha-amino acid peptides[1] has stimulated considerable interest in the...
Venkatraman, Janani, Gowda, Nagana GA, Balaram, Padmanabhan
EmrE, a multidrug resistance protein from Escherichia coli, renders the bacterium resistant to a variety of cytotoxic drugs by active translocation out of the cell. The 110-residue sequence of EmrE...
Venkatraman, Janani, Gowda, Nagana GA, Balaram, Padmanabhan
The design and characterization of an open eight- stranded ‚beta-sheet in a synthetic, 2- fold symmetric 70-residue peptide is described. The design strategy involves the generation of a 35-residue...
Karle, Isabella, Gopi, Hosahudya N, Balaram, Padmanabhan
A beta-hairpin conformation and extended beta-pleated sheet assembly have been characterized by single crystal x-ray diffraction for the synthetic peptide...
De novo design of a five-stranded beta-sheet anchoring a metal-ion binding site (2001)
Venkatraman, Janani, Naganagowda, GA, Sudha, R, Balaram, Padmanabhan
A five-stranded beta-sheet bearing two histidine residues as part of a metal-binding site has been designed, synthesized and characterised using NMR and electrospray ionization mass spectrometry...
Ab initio structure determination of a peptide beta-turn from powder X-ray diffraction data (2001)
Tedesco, Emilio, Harris, Kenneth DM, Johnston, Roy L, Turner, Giles W, Raja, Muruga Poopathi K, Balaram, Padmanabhan
Ab initio crystal structure determination of the peptide Piv-Pro-Gly-NHMe directly from powder X-ray diffraction data, using the genetic algorithm technique for structure solution, has allowed the...
Design of Folded Peptides (2001)
Venkatraman, Janani, Shankaramma, Sasalu C, Balaram, Padmanabhan
The construction of complex protein folds relies on the precise conversion of a linear polypeptide chain into a compact 3-dimensional structure. The interplay of forces that link sequence and folding...
Karle, Isabella L, Gopi, Hosahudya N, Balaram, Padmanabhan
A beta-hairpin conformation has been characterized in crystals of the decapeptide t-butoxycarbonyl-Leu-Val-betaPhe-Val-DPro-Gly-Leub Phe-Val-Val-methyl ester [bPhe; (S)-b3 homophenylalanine] by x-ray...
Molecular Carpentry: Piecing Together Helices and Hairpins in Designed Peptides (2001)
Das, Chittaranjan, Shankaramma, Channaveerappa S, Balaram, Padmanabhan
The design of a peptide that contains two distinct elements of secondary structure, helix and beta-hairpin, is described. Two designed 17-residue peptides:...
Karle, Isabella L, Das, Chittaranjan, Balaram, Padmanabhan
The Meccano (or Lego) set approach to synthetic protein design envisages covalent assembly of prefabricated units of peptide secondary structure. Stereochemical control over peptide folding is...
Prasanna, Variath, Gopal, B, Murthy, MRN, Santi, Daniel V, Balaram, Padmanabhan
The significance of two interface arginine residues on the structural integrity of an obligatory dimeric enzyme thymidylate synthase (TS) from Lactobacillus casei was investigated by thermal and...
Karle, Isabella L, Perozzo, Mary Ann, Mishra, Vinod K, Balaram, Padmanabhan
Crystals of an ion-channel-forming peptaibol peptide in a partial membrane environment have been obtained by cocrystallizing antiamoebin with n-octanol. The antiamoebin molecule has a bent helical...
Prasanna, Variath, Bhattacharjya, Surajit, Balaram, Padmanabhan
Three synthetic peptides corresponding to distinct segments of the subunit interface of the dimeric enzyme thymidylate synthase (residues 17-38, N 22; residues 174-190, M 17; and residues 201-220, C...
Raghothama, Srinivasa Rao, Awasthi, Satish Kumar, Balaram, Padmanabhan
The solution conformation of the synthetic octapeptide Boc-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe 1 and Boc-Leu-Val-Val-Pro-Gly-Leu-Val-Val-OMe 2 have been investigated in organic solvents by NMR...
Bhattacharjya, Surajit, Awasthi, Satish K, Adiga, Radhakantha P, Balaram, Padmanabhan
Riboflavin carrier protein (RCP) plays an important role in transporting vitamin B2 across placental membranes, a process critical for maintenance of pregnancy. Association of the vitamin with the...
Bhattacharjya, Surajit, Balaram, Padmanabhan
A molten globule-like state of hen egg-white lysozyme has been characterized in 25% aqueous hexafluoroacetone hydrate (HFA) by CD, fluorescence, NMR, and H/D exchange experiments. The far UV CD...
Banerjee, Arindam, Raghothama, Srinivasa Rao, Karle, Isabella L, Balaram, Padmanabhan
The handedness or chirality of molecules, organisms, and elementary particles has been widely appreciated, vindicating Pasteur’s perceptive generalization, “L‘uni-vers est dissymktrique.‿...
Awasthi, Satish Kumar, Raghothama, Srinivasa Rao, Balaram, Padmanabhan
The conformational characteristics of three hexapeptides Boc-Leu-Xxx-Val-Leu-Aib-Val-OMe(Xxx = Ala 1, D-Ala2, Gly 3; Aib =alpha-aminoisobutyryl) have been probed in CDCl3 solution by NMR methods...
A designed beta-hairpin peptide in crystals (1996)
Karle, Isabella L, Awasthi, Satish K, Balaram, Padmanabhan
Beta-hairpin structures have been crystallographically characterized only in very short acyclic peptides, in contrast to helices. The structure of the designed beta-hairpin,...
Gokhale, Rajesh S, Agarwalla, Sanjay, Santi, Daniel V, Balaram, Padmanabhan
Urea and guanidinium chloride induced unfolding of thymidylate synthase, a dimeric enzyme, and engineered interface mutants have been monitored by circular dichroism, fluorescence, and sizeexclusion...
Non-standard amino acids in peptide design and protein engineering (1992)
The introduction of non-coded amino acids with well defined stereochemical and functional properties will greatly enhance the scope of protein design and engineering. The present state of...
Karle, Isabella L, Flippen-Anderson, Judith L, Agarwalla, Sanjay, Balaram, Padmanabhan
Structures in four different crystal forms of [Leu1]zervamicin (zervamicin Z-L, Ac-Leu-Ile-Gln-Iva-Ile5-Thr-Aib-Leu-Aib-Hyp10-Gln-Aib -Hyp-Aib- Pro15-Phol, where Iva is isovaline, Aib is \alpha-amino...